Great points. That's pretty much where my thoughts were going.
People seem to be thinking this thorough as a parallel to what we think of as cyber attacks in the internet world today where viruses and trojans take control of our PCs for nefarious purposes. And while that may be desirable to the Navy too, everything in warfare is moving toward digital communications these days. There are a number of types of tactical data links, communicating virtually everything that one battlefield entity might need to know from another and it's only going to get more widespread over time.
You don't need to "take over" an enemy radar when you can just tell it to report whatever you want to its operator via spoofed waveforms. Or, if a good guy plane could fool others into thinking it was an enemy plane (with a spoofed radar signature, IFF, etc.), the benefits are obvious.
The difficulties are defeating encryption and decoding messages/waveforms to be able to inject specific bits of data as seen fit. Though, a targeted DoS attack is probably not very difficult to achieve even now because if you flood a link with messages of the appropriate size, it still has to do some processing to decide that it can't do anything with them, possibly slowing or stopping legitimate messages.
Incidentally, I work in defense and I don't see my company listed in TFA so that sucks because this would be an interesting project. Though, it might be involved in some way that I just don't know about (because it's a huge company, not necessarily because of secrecy or anything).